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MSAs and corresponding indel character matrices for the first 40 amino acids of the human AGPS gene (ENSG00000018510) as inferred by (A) PRANK, (B) MAFFT, and (C) CLUSTALW. Homoplasious indels, which conflict the accepted primate tree, are boxed in yellow. The three alignment methods highly disagree on the placement of these indels. RELINDEL identifies these indels as highly unreliable (see text).
